Gaddle Maps
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GADDLE Maps simplified documentation
gaddlemaps package
Gaddle Maps
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Index
A
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B
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C
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D
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E
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F
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G
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I
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
A
accept_metropolis() (in module gaddlemaps)
add_end_molecule() (gaddlemaps.Manager method)
add_end_molecules() (gaddlemaps.Manager method)
add_ftop() (gaddlemaps.components.System method)
add_molecule_top() (gaddlemaps.components.System method)
align_molecules() (gaddlemaps.Alignment method)
(gaddlemaps.Manager method)
Alignment (class in gaddlemaps)
are_connected() (in module gaddlemaps.components)
Atom (class in gaddlemaps.components)
atom_gro (gaddlemaps.components.Atom property)
atom_top (gaddlemaps.components.Atom property)
AtomGro (class in gaddlemaps.components)
atomid (gaddlemaps.components.AtomGro attribute)
atoms (gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
atoms_ids (gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
atoms_positions (gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
atoms_velocities (gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
AtomTop (class in gaddlemaps.components)
B
bonds (gaddlemaps.components.AtomTop attribute)
bonds_distance (gaddlemaps.components.Molecule property)
box_matrix (gaddlemaps.components.SystemGro property)
(gaddlemaps.parsers.CoordinatesParser property)
(gaddlemaps.parsers.GroFile property)
C
calculate_exchange_maps() (gaddlemaps.Manager method)
calcule_base() (in module gaddlemaps)
chi2_molecules() (gaddlemaps.Chi2Calculator method)
Chi2Calculator (class in gaddlemaps)
close() (gaddlemaps.parsers.CoordinatesParser method)
(gaddlemaps.parsers.GroFile method)
closest_atoms() (gaddlemaps.components.AtomTop method)
comment (gaddlemaps.parsers.CoordinatesParser property)
(gaddlemaps.parsers.GroFile property)
comment_line (gaddlemaps.components.SystemGro property)
complete_correspondence (gaddlemaps.Manager property)
composition (gaddlemaps.components.System property)
(gaddlemaps.components.SystemGro property)
connect() (gaddlemaps.components.AtomTop method)
COORD_START (gaddlemaps.parsers.GroFile attribute)
CoordinatesParser (class in gaddlemaps.parsers)
copy() (gaddlemaps.components.Atom method)
(gaddlemaps.components.AtomGro method)
(gaddlemaps.components.AtomTop method)
(gaddlemaps.components.Molecule method)
(gaddlemaps.components.MoleculeTop method)
(gaddlemaps.components.Residue method)
D
deep_copy() (gaddlemaps.components.Molecule method)
DEFAULT_COMMENT (gaddlemaps.parsers.GroFile attribute)
DEFAULT_POSTION_FORMAT (gaddlemaps.parsers.GroFile attribute)
determine_format() (gaddlemaps.parsers.GroFile class method)
distance_to() (gaddlemaps.components.Molecule method)
(gaddlemaps.components.Residue method)
distance_to_zero (gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
dump_lattice_gro() (in module gaddlemaps.parsers)
E
element (gaddlemaps.components.AtomGro property)
end (gaddlemaps.Alignment property)
equivalences (gaddlemaps.ExchangeMap property)
exchange_map (gaddlemaps.Alignment attribute)
ExchangeMap (class in gaddlemaps)
EXTENSIONS (gaddlemaps.parsers.CoordinatesParser attribute)
(gaddlemaps.parsers.GroFile attribute)
extract_lattice_gro() (in module gaddlemaps.parsers)
extrapolate_system() (gaddlemaps.Manager method)
F
fgro (gaddlemaps.components.System property)
find_atom_random_displ() (in module gaddlemaps)
from_files() (gaddlemaps.components.Molecule class method)
(gaddlemaps.Manager class method)
G
gaddlemaps
module
gaddlemaps.components
module
gaddlemaps.parsers
module
geometric_center (gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
gro_line() (gaddlemaps.components.AtomGro method)
gro_resid (gaddlemaps.components.Atom property)
GroFile (class in gaddlemaps.parsers)
guess_protein_restrains() (in module gaddlemaps)
guess_residue_restrains() (in module gaddlemaps)
I
index() (gaddlemaps.components.Molecule method)
(gaddlemaps.components.MoleculeTop method)
init_exchange_map() (gaddlemaps.Alignment method)
interactive_restrictions() (gaddlemaps.Alignment method)
(gaddlemaps.Manager method)
(in module gaddlemaps)
M
Manager (class in gaddlemaps)
minimize_molecules() (in module gaddlemaps)
module
gaddlemaps
gaddlemaps.components
gaddlemaps.parsers
Molecule (class in gaddlemaps.components)
molecule_correspondence (gaddlemaps.Manager attribute)
molecule_top (gaddlemaps.components.Molecule property)
molecules_info_ordered_all (gaddlemaps.components.SystemGro property)
molecules_resname_len_index (gaddlemaps.components.SystemGro property)
MoleculeTop (class in gaddlemaps.components)
move() (gaddlemaps.components.Molecule method)
(gaddlemaps.components.Residue method)
move_mol_atom() (in module gaddlemaps)
move_to() (gaddlemaps.components.Molecule method)
(gaddlemaps.components.Residue method)
mro() (gaddlemaps.parsers.ParserRegistered method)
N
n_atoms (gaddlemaps.components.SystemGro property)
name (gaddlemaps.components.AtomGro attribute)
(gaddlemaps.parsers.GroFile property)
natoms (gaddlemaps.parsers.CoordinatesParser property)
(gaddlemaps.parsers.GroFile property)
next() (gaddlemaps.parsers.CoordinatesParser method)
(gaddlemaps.parsers.GroFile method)
NUMBER_FIGURES (gaddlemaps.parsers.GroFile attribute)
O
open_coordinate_file() (in module gaddlemaps.parsers)
P
parse_atomline() (gaddlemaps.parsers.GroFile class method)
parse_atomlist() (gaddlemaps.parsers.GroFile class method)
parse_restrictions() (gaddlemaps.Manager method)
ParserManager (class in gaddlemaps.parsers)
ParserRegistered (class in gaddlemaps.parsers)
parsers (gaddlemaps.parsers.ParserManager attribute)
position (gaddlemaps.components.AtomGro attribute)
position_format (gaddlemaps.parsers.GroFile property)
R
readline() (gaddlemaps.parsers.GroFile method)
readlines() (gaddlemaps.parsers.GroFile method)
register() (gaddlemaps.parsers.ParserManager class method)
(gaddlemaps.parsers.ParserRegistered method)
remove_atom() (gaddlemaps.components.Molecule method)
(gaddlemaps.components.Residue method)
remove_hydrogens() (in module gaddlemaps)
resid (gaddlemaps.components.AtomGro attribute)
(gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
residname (gaddlemaps.components.AtomGro property)
(gaddlemaps.components.AtomTop property)
(gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
resids (gaddlemaps.components.Molecule property)
(gaddlemaps.components.MoleculeTop property)
Residue (class in gaddlemaps.components)
residues (gaddlemaps.components.Molecule property)
resname (gaddlemaps.components.AtomGro attribute)
(gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
resname_len_list (gaddlemaps.components.MoleculeTop property)
resnames (gaddlemaps.components.Molecule property)
(gaddlemaps.components.MoleculeTop property)
rotate() (gaddlemaps.components.Molecule method)
(gaddlemaps.components.Residue method)
rotation_matrix() (in module gaddlemaps)
S
seek_atom() (gaddlemaps.parsers.CoordinatesParser method)
(gaddlemaps.parsers.GroFile method)
SIGMA_SCALE (gaddlemaps.Alignment attribute)
,
[1]
start (gaddlemaps.Alignment property)
STEPS_FACTOR (gaddlemaps.Alignment attribute)
,
[1]
System (class in gaddlemaps.components)
SystemGro (class in gaddlemaps.components)
T
top_resid (gaddlemaps.components.Atom property)
U
update_from_molecule_top() (gaddlemaps.components.Molecule method)
(gaddlemaps.components.Residue method)
V
validate_string() (gaddlemaps.parsers.GroFile static method)
velocity (gaddlemaps.components.AtomGro attribute)
W
write_comparative_gro() (gaddlemaps.Alignment method)
write_gro() (gaddlemaps.components.Molecule method)
(gaddlemaps.components.Residue method)
writeline() (gaddlemaps.parsers.CoordinatesParser method)
(gaddlemaps.parsers.GroFile method)
writelines() (gaddlemaps.parsers.CoordinatesParser method)
(gaddlemaps.parsers.GroFile method)
X
x (gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
Y
y (gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
Z
z (gaddlemaps.components.Molecule property)
(gaddlemaps.components.Residue property)
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